Chromosomal Abnormalities of Interest in Turner Syndrome: An Update.

Turner syndrome (TS) is caused by the total or partial loss of the second sex chromosome; it occurs in 1 every 2,500-3,000 live births. The clinical phenotype is highly variable and includes short stature and gonadal dysgenesis. In 1959, the chromosomal origin of the syndrome was recognized; patients had 45 chromosomes with a single X chromosome. TS presents numerical and structural abnormalities in the sex chromosomes, interestingly only 40% have a 45, X karyotype. The rest of the chromosomal abnormalities include mosaics, deletions of the short and long arms of the X chromosome, rings, and isochromosomes. Despite multiple studies to establish a relationship between the clinical characteristics and the different chromosomal variants in TS, a clear association cannot yet be established. Currently, different mechanisms involved in the phenotype have been explored. This review focuses to analyze the different chromosomal abnormalities and phenotypes in TS and discusses the possible mechanisms that lead to these abnormalities.

Molecular Characterization of Associated Pathogens in Febrile Patients during Inter-Epidemic Periods of Urban Arboviral Diseases in Tapachula Southern Mexico.

Emerging and re-emerging vector-borne infections are a global public health threat. In endemic regions, fever is the main reason for medical attention, and the etiological agent of such fever is not usually identified. In this study, non-specific febrile pathogens were molecularly characterized in serum samples from 253 patients suspected of arbovirus infection. The samples were collected in the southern border region of Mexico from April to June 2015, and February to March 2016. ZIKV, CHIKV, DENV, leptospirosis, and rickettsiosis were detected by qPCR and nested PCR to identify flavivirus and alphavirus genera. The results indicated that 71.93% of the samples were positive for CHIKV, 0.79% for ZIKV, and 0.39% for DENV, with the number positive for CHIKV increasing to 76.67% and those positive for ZIKV increasing to 15.41% under the nested PCR technique. Leptospira Kmetyi was identified for the first time in Mexico, with a prevalence of 3.16%. This is the first report of ZIKV in Mexico, as well the first detection of the virus in early 2015. In conclusion, the etiological agent of fever was determined in 94% of the analyzed samples.

A case series of infants with increased VAMP7 gene dosage at birth and virilization defects.

BACKGROUND: Genitourinary disorders are the most frequent congenital defects in newborns; however, little is known about their etiology. Several studies have been carried out to find genetic risk factors in the development of these malformations. The expression of VAMP7 is found in testes, epididymis, seminal vesicles, prostatic tissues, penis, and urethra. Alterations in gene dose of VAMP7 were recently reported in a subset of male patients initially identified clinically by the presence of congenital genitourinary disorders. In 2016, the authors developed a diagnostic algorithm for early detection of sex chromosome aneuploidies by quantifying the SHOX, VAMP7, and SRY gene dose in newborns by qPCR using dried blood spot (DBS) samples. OBJECTIVE: Correlate the increased gene dose of VAMP7, obtained by qPCR using DBS, with genitourinary congenital defects attributable to disorders in virilization and verify the increased gene dose by microarrays. STUDY DESIGN: Samples that only presented increased VAMP7 gene dosage were selected from a previously analyzed group of 5088 males in which the early detection of sex chromosomes aneuploidies was performed. Eight males were found with an increased gene dose of VAMP7 (relative quantitation > 1.3) and were called in for a complete clinical evaluation aimed at the identification of genitourinary anomalies, qPCR and microarrays. RESULTS: Eight males from 5088 samples were identified with increased VAMP7 gene dosage of which six patients were clinically evaluated, of which 50% were identified with alterations in genital development (bilateral cryptorchidism, unilateral cryptorchidism, and glandular hypospadias) and speech delay, while the rest presented different types of atopy. DISCUSSION: Tannour-Louet et al. postulated on 2014 that the duplication of the Xq28 region, specifically of VAMP7, plays a role in the human masculinization disorders of the urogenital tract. The study was based on array comparative genomic hybridization (aCGH) results performed to 116 males with disorders of sexual differentiation. In the present study, the patients were initially selected due to an increased gene dose of VAMP7 detected by qPCR, then the clinical evaluation and the aCGH were performed, inverse to what was reported previously but with similar percentages between both studies. CONCLUSION: In this work, the authors report cases of cryptorchidism, hypospadias, language delay and atopy in male preschoolers initially identified because they have an increased gene dose of VAMP7.

Gene Copy Number Quantification of SHOX, VAMP7, and SRY for the Detection of Sex Chromosome Aneuploidies in Neonates.

Aims: To explore the feasibility of detecting sex chromosome aneuploidies (SCAs) by means of gene copy number quantification of short stature homeobox (SHOX), vesicle-associated membrane protein 7 (VAMP7), and SRY in newborns. Materials and Methods: Gene doses of SHOX, VAMP7, and SRY were determined by quantitative polymerase chain reaction (qPCR) using DNA obtained from dried blood samples from newborns. Relative quantification values were obtained. An aneuploidy profile was established according to cutoff values. Samples with ≥2 gene doses (out of range) were reanalyzed, and those with aneuploidy profiles were confirmed by karyotyping. Sensitivity, specificity, and positive and negative predictive values were obtained. Results: A total of 10,033 samples were collected (4945 females and 5088 males). Of 244 (2.43%) samples with ≥2 gene doses that were retested, 20 cases were confirmed. The overall incidence of SCAs was 1 in 500 live newborns. There were six cases of Turner syndrome (1/824), 3 cases of XXX (1/1648), 7 cases of Klinefelter syndrome (1/726), and 4 cases of of XYY (1/1272). The sensitivity was 0.952 (95.42%); the specificity was 0.975 (97.56%); the positive predictive value was 0.909 (90.91%) and the negative predictive value was 0.987 (98.77%). Conclusions: Gene copy number analyses of the VAMP7, SHOX, and SRY genes by qPCR from blood samples spotted onto filter paper is a highly reliable method for the early detection of male and female SCAs.

Analysis of the pathogenic variants of BRCA1 and BRCA2 using next-generation sequencing in women with familial breast cancer: a case-control study.

BACKGROUND: Pathogenic variants (PVs) of BRCA genes entail a lifetime risk of developing breast cancer in 50-85% of carriers. Their prevalence in different populations has been previously reported. However, there is scarce information regarding the most common PVs of these genes in Latin-Americans. This study identified BRCA1 and BRCA2 PV frequency in a high-risk female population from Northeastern Mexico and determined the association of these mutations with the patients' clinical and pathological characteristics. METHODS: Women were divided into three groups: aged ≤ 40 years at diagnosis and/or risk factors for hereditary breast cancer (n = 101), aged > 50 years with sporadic breast cancer (n = 22), and healthy women (n = 72). Their DNA was obtained from peripheral blood samples and the variants were examined by next-generation sequencing with Ion AmpliSeq BRCA1 and BRCA2 Panel using next-generation sequencing. RESULTS: PVs were detected in 13.8% group 1 patients (BRCA1, 12 patients; BRCA2, 2 patients). Only two patients in group 2 and none in group 3 exhibited BRCA1 PVs. Variants of uncertain significance were reported in 15.8% patients (n = 16). In group 1, patients with the triple-negative subtype, PV frequency was 40% (12/30). Breast cancer prevalence in young women examined in this study was higher than that reported by the National Cancer Institute Surveillance, Epidemiology (15.5% vs. 5.5%, respectively). CONCLUSIONS: The detected BRCA1 and BRCA2 PV frequency was similar to that reported in other populations. Our results indicate that clinical data should be evaluated before genetic testing and highly recommend genetic testing in patients with the triple-negative subtype and other clinical aspects.

Phenotypic Variation in Patients with Homozygous c.1678G>T Mutation in EVC Gene: Report of Two Mexican Families with Ellis-van Creveld Syndrome.

BACKGROUND Ellis-van Creveld syndrome is an autosomal recessive chondro-ectodermal dysplasia characterized by disproportionate short stature, limb shortening, narrow chest, postaxial polydactyly and dysplastic nails and teeth. In addition, 60% of cases present congenital heart defects. Ellis-van Creveld syndrome is predominantly caused by mutations in the EVC or EVC2 (4p16) genes, with only a few cases caused by mutations in WDR35.  CASE REPORT Here, we report on two Mexican families with patients diagnosed with Ellis-van Creveld syndrome. Family 1 includes four patients: three females of 15, 18, and 23 years of age and a 7-year old male. Family 2 has only one affected newborn male. All patients exhibited multiple features including hypodontia, dysplastic teeth, extra frenula, mild short stature, distal limb shortening, postaxial polydactyly of hands and feet, nail dystrophy, and knee joint abnormalities. Only two patients had an atrial septal defect. In all cases, molecular analysis by Sanger sequencing identified the same homozygous mutation in exon 12 of EVC, c.1678G>T, which leads to a premature stop codon.  CONCLUSIONS The mutation c.1678G>T has been previously reported in another Mexican patient and it appears to be a recurrent mutation in Mexico which could represent a founder mutation. The large number of patients in this case allows the clinical variability and spectrum of manifestations present in individuals with Ellis-van Creveld syndrome even if they carry the same homozygous mutation in a same family.

Dosage of Sex Chromosomal Genes in Blood Deposited on Filter Paper for Neonatal Screening of Sex Chromosome Aneuploidy.

AIMS: In this study, we examined the doses of the stature homeobox (SHOX), vesicle-associated membrane protein 7 (VAMP7), and SRY genes to establish a protocol for using peripheral blood samples deposited on filter paper for the screening of sex chromosome aneuploidy in neonates. We also measured correlations with karyotypes to assess this method as a neonatal screening strategy. MATERIALS AND METHODS: This was an observational, descriptive, comparative blind study. Thirty-two healthy young adults (17 women, 15 men; age, ≥18 years), four patients with known sex chromosome aneuploidy (positive control group), and 1000 healthy newborns were included. Gene dosages were determined using quantitative real-time polymerase chain reaction (RT-PCR). Values with standard deviations (SDs) of three or more were considered abnormal. RESULTS: Men and women differed in the gene dosage of the SRY gene. Cases with Turner syndrome showed values below 3 SDs for SHOX and VAMP7 genes, and cases with Klinefelter syndrome showed values above 3 SDs for SHOX and VAMP7 genes. Two suspected cases of sex chromosome aneuploidy were diagnosed using our neonatal screening strategy; these cases were confirmed as Turner syndrome and 47,XYY syndrome by karyotyping. CONCLUSIONS: Our data establish a basis for the determination of chromosomal sex and neonatal screening of sex chromosome aneuploidy using RT-PCR.

Detection of Turner Syndrome by quantitative PCR of SHOX and VAMP7 genes.

Turner Syndrome (TS) is an unfavorable genetic condition with a prevalence of 1:2500 in newborn girls. Prompt and effective diagnosis is very important to appropriately monitor the comorbidities. The aim of the present study was to propose a feasible and practical molecular diagnostic tool for newborn screening by quantifying the gene dosage of the SHOX, VAMP7, XIST, UBA1, and SRY genes by quantitative polymerase chain reaction (qPCR) in individuals with a diagnosis of complete X monosomy, as well as those with TS variants, and then compare the results to controls without chromosomal abnormalities. According to our results, the most useful markers for these chromosomal variants were the genes found in the pseudoautosomic regions 1 and 2 (PAR1 and PAR2), because differences in gene dosage (relative quantification) between groups were more evident in SHOX and VAMP7 gene expression. Therefore, we conclude that these markers are useful for early detection in aneuploidies involving sex chromosomes.

GJB2 and GJB6 mutations are an infrequent cause of autosomal-recessive nonsyndromic hearing loss in residents of Mexico.

OBJECTIVES: Mutations in the DFNB1 locus are the most common cause of autosomal-recessive nonsyndromic hearing loss (ARNSHL) worldwide. The aim of this study was to identify the most frequent mutations in patients with ARNSHL who reside in Northeastern Mexico. METHODS: We determined the nucleotide sequence the coding region of GJB2 of 78 patients with ARNSHL. Polymerase chain reaction assays were used to detect the GJB2 IVS1+1G>A mutation and deletions within GJB6. RESULTS: GJB2 mutations were detected in 9.6% of the alleles, and c.35delG was the most frequent. Six other less-frequent mutations were detected, including an extremely rare variant (c.645_648delTAGA), a novel mutation (c.35G>A), and one of possible Mexican origin (c.34G>T). GJB6 deletions and GJB2 IVS1+1G>A were not detected. CONCLUSIONS: These data suggest that mutations in the DFNB1 locus are a rare cause of ARNSHL among the population of Northeastern Mexico. This confirms the genetic heterogeneity of this condition and indicates that further research is required to determine the other mechanisms of pathogenesis of ARNSHL in Mexicans.

Nueva mutación en el gen RAB27A en una familia mexicana con Síndrome de Griscelli tipo 2 / New RAB27A gene mutation in a Mexican family with type 2 Griscelli syndrome

El síndrome de Griscelli (SG) es una enfermedad autosómica recesiva, caracterizada, según las variantes clínicas, por albinismo parcial o cabello platinado, inmunodeficiencia celular, hipogammaglobulinemia, pancitopenia y severo deterioro neurológico. El diagnóstico se realiza de acuerdo a los hallazgos histopatológicos de la biopsia de piel, las manifestaciones clínicas descriptas y el análisis molecular de los genes RAB27A y MYO5A. Se describe un caso de SG, confirmado mediante estudio molecular, en una familia mexicana con antecedentes de consanguinidad tío paterno-sobrina y una hermana mayor con característiscas similares, fallecida a los 4 años. El paciente, al nacer, había tenido diagnóstico de albinismo. Se presentó a la consulta con historia de infecciones frecuentes y fiebres recurrentes sin foco y se encontró bicitopenia y síndrome mieloproliferativo. Ante la sospecha diagnóstica, se realizó una microscopía del cabello, en la que se observó distribución del pigmento en cúmulos y en los frotis hemáticos se determinó la ausencia de inclusiones intracitoplasmáticas. Se estableció el diagnóstico de SG tipo 2 y se obtuvo una muestra de ADN para el estudio molecular del gen RAB27A. El examen confirmó una mutación homocigota no comunicada previamente, por lo que se dedujo que su hermana había tenido la misma afección y que el padre era portador obligado...

Griscelli syndrome (GS) is an autosomal recessive disease characterized by partial albinism or platinum hair, varying cell immunodeficiency, hypogammaglobulinemia, pancytopenia and severe neurological impairment, depending on clinical variants. The diagnosis is made with histopathological findings in skin biopsy, the clinical manifestations described and molecular analysis of the genes RAB27A and MYO5A. We describe a case of GS, confirmed by molecular study, in a Mexican family with a history of paternal uncle-niece consanguinity and a sister with similar characteristics, deceased at 4 years old. At birth, the patient was diagnosed as albinism. He presented to us with a history of frequent infections and recurrent fevers of unknown origin and a bicytopenia and a myeloproliferative syndrome were found. With diagnostic suspicion, a mycroscopic study of the hair was done and the findings were consistent with pigment distribution in clusters and in hematological smears the absence of intracytoplasmic inclusions was demonstrated. Therefore the diagnosis of GS type 2 was established and a DNA sample was obtained for RAB27A gene molecular study. The exam confirmed a previously unreported homozygous mutation in the gene RAB27A, so it was established that his sister had the same condition and the father was a forced carrier...

Nueva mutación en el gen RAB27A en una familia mexicana con Síndrome de Griscelli tipo 2 / New RAB27A gene mutation in a Mexican family with type 2 Griscelli syndrome

El síndrome de Griscelli (SG) es una enfermedad autosómica recesiva, caracterizada, según las variantes clínicas, por albinismo parcial o cabello platinado, inmunodeficiencia celular, hipogammaglobulinemia, pancitopenia y severo deterioro neurológico. El diagnóstico se realiza de acuerdo a los hallazgos histopatológicos de la biopsia de piel, las manifestaciones clínicas descriptas y el análisis molecular de los genes RAB27A y MYO5A. Se describe un caso de SG, confirmado mediante estudio molecular, en una familia mexicana con antecedentes de consanguinidad tío paterno-sobrina y una hermana mayor con característiscas similares, fallecida a los 4 años. El paciente, al nacer, había tenido diagnóstico de albinismo. Se presentó a la consulta con historia de infecciones frecuentes y fiebres recurrentes sin foco y se encontró bicitopenia y síndrome mieloproliferativo. Ante la sospecha diagnóstica, se realizó una microscopía del cabello, en la que se observó distribución del pigmento en cúmulos y en los frotis hemáticos se determinó la ausencia de inclusiones intracitoplasmáticas. Se estableció el diagnóstico de SG tipo 2 y se obtuvo una muestra de ADN para el estudio molecular del gen RAB27A. El examen confirmó una mutación homocigota no comunicada previamente, por lo que se dedujo que su hermana había tenido la misma afección y que el padre era portador obligado...(AU)

Griscelli syndrome (GS) is an autosomal recessive disease characterized by partial albinism or platinum hair, varying cell immunodeficiency, hypogammaglobulinemia, pancytopenia and severe neurological impairment, depending on clinical variants. The diagnosis is made with histopathological findings in skin biopsy, the clinical manifestations described and molecular analysis of the genes RAB27A and MYO5A. We describe a case of GS, confirmed by molecular study, in a Mexican family with a history of paternal uncle-niece consanguinity and a sister with similar characteristics, deceased at 4 years old. At birth, the patient was diagnosed as albinism. He presented to us with a history of frequent infections and recurrent fevers of unknown origin and a bicytopenia and a myeloproliferative syndrome were found. With diagnostic suspicion, a mycroscopic study of the hair was done and the findings were consistent with pigment distribution in clusters and in hematological smears the absence of intracytoplasmic inclusions was demonstrated. Therefore the diagnosis of GS type 2 was established and a DNA sample was obtained for RAB27A gene molecular study. The exam confirmed a previously unreported homozygous mutation in the gene RAB27A, so it was established that his sister had the same condition and the father was a forced carrier...(AU)

Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements.

Complex genomic rearrangements (CGRs) consisting of two or more breakpoint junctions have been observed in genomic disorders. Recently, a chromosome catastrophe phenomenon termed chromothripsis, in which numerous genomic rearrangements are apparently acquired in one single catastrophic event, was described in multiple cancers. Here, we show that constitutionally acquired CGRs share similarities with cancer chromothripsis. In the 17 CGR cases investigated, we observed localization and multiple copy number changes including deletions, duplications, and/or triplications, as well as extensive translocations and inversions. Genomic rearrangements involved varied in size and complexities; in one case, array comparative genomic hybridization revealed 18 copy number changes. Breakpoint sequencing identified characteristic features, including small templated insertions at breakpoints and microhomology at breakpoint junctions, which have been attributed to replicative processes. The resemblance between CGR and chromothripsis suggests similar mechanistic underpinnings. Such chromosome catastrophic events appear to reflect basic DNA metabolism operative throughout an organism's life cycle.